iTRAQ-based proteomic analysis of bovine pre-ovulatory plasma and follicular fluid

Unveiling the power of proteomics in advancing tropical animal health and production

Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.

Characterization of preovulatory follicular fluid secretome and its effects on equine oocytes during in vitro maturation

In vitro maturation (IVM) of oocytes is clinically used in horses to produce blastocysts but current conditions used for horses are suboptimal. We analyzed the composition of equine preovulatory follicular fluid (FF) secretome and tested its effects on meiotic competence and gene expression in oocytes subjected to IVM. Preovulatory FF was obtained, concentrated using ultrafiltration with cut-off of 10 kDa, and stored at -80 °C. The metabolic and proteomic composition was analyzed, and its ultrastructural composition was assessed by cryo-transmission microscopy. Oocytes obtained post-mortem or by ovum pick up (OPU) were subjected to IVM in the absence (control) or presence of 20 or 40 μg/ml (S20 or S40) of secretome. Oocytes were then analyzed for chromatin configuration or snap frozen for gene expression analysis. Proteomic analysis detected 255 proteins in the Equus caballus database, mostly related to the complement cascade and cholesterol metabolism. Metabolomic analysis yielded 14 metabolites and cryo-transmission electron microscopy analysis revealed the presence of extracellular vesicles (EVs). No significant differences were detected in maturation rates among treatments. However, the expression of GDF9 and BMP15 significantly increased in OPU-derived oocytes compared to post-mortem oocytes (fold increase ± SEM: 9.4 ± 0.1 vs. 1 ± 0.5 for BMP15 and 9.9 ± 0.3 vs. 1 ± 0.5 for GDF9, respectively; p < 0.05). Secretome addition increased the expression of TNFAIP6 in S40 regardless of the oocyte source. Further research is necessary to fully understand whether secretome addition influences the developmental competence of equine oocytes.

Prolonged follicular dominance is associated with dysregulated proteomic profile of the follicular fluid in Bos indicus cows

Prolonged follicular dominance is one of the conditions associated with disconcerted follicular dynamics that result in substantial economic losses to the farmers through low reproductive efficiency in cattle. Hormonal aberrations associated with prolonged follicular dominance may affect the follicular microenvironment and composition of follicular fluid. The current study focused on proteome changes of follicular fluid in prolonged follicular dominance compared to physiological follicular dominance. Prolonged dominance was induced in Deoni cows (n = 6) by using CIDR (previously used for 7 days) from day 4-8 of estrus, with PGF2 injection on day 6 and day 7 at 12 h intervals. Follicular fluid was collected by ultrasound guided transvaginal follicular aspiration method. Global proteomic analysis of follicular fluid revealed 217 proteins in the Deoni cow, with the majority of proteins involved in 21 pathways, 42 molecular functions, and 106 biological processes. Complement and coagulation cascades (22.8%) and cholesterol metabolism (4.68%) were the major pathways in which identified proteins were involved. Comparison of physiological and prolonged dominant follicular fluid revealed differential expression of 26 proteins, of which 15 were upregulated and 11 were downregulated. Proteins involved in complement and coagulation cascades, and vitamin digestion and absorption were found to be dysregulated in PFD. The present study suggests that the expression of proteins involved in inflammation, oocyte metabolism, and ovulation cascade were found to be dysregulated in the follicular fluid of prolonged follicular dominance consequently resulting in delayed ovulation or anovulation.

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle-A Review

Female fertility is the foundation of the cow-calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow-calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.

Metabolite abundance in bovine preovulatory follicular fluid is influenced by follicle developmental progression post estrous onset in cattle

Introduction: Preovulatory follicle response to the luteinizing hormone (LH) surge leads to metabolic, molecular, and functional changes in the oocyte and somatic follicular cells from the onset of estrus to ovulation. Follicular fluid contains metabolites, miRNAs, proteins, and hormones that are byproducts of follicular metabolism and support cellular processes of oocyte, cumulus, and granulosa constituents. Numerous studies have highlighted the importance of follicular fluid composition to support fertility, but critical gaps exist toward understanding dynamic modifications in the follicular fluid metabolome from estrous onset to ovulation. The hypothesis was that abundance of follicular fluid metabolites is dependent on follicle progression post LH surge and variability in follicular fluid metabolome profiles indicate key processes required for preparation of the follicle and oocyte for optimal fertility. The objective was to generate preovulatory follicular fluid metabolome profiles and discern differences in the metabolome of preovulatory follicular fluid samples collected at onset of estrus, 11 h post estrous onset, and 18 h post estrous onset. Methods: Estrus was synchronized in non-lactating Jersey cows (n=40) and follicular fluid was collected immediately after the first observed standing mount (hr 0) or at approximately h 11 or 18 after the first standing mount. Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry was performed on preovulatory follicular fluid samples (n = 9 collected at hr 0, 9 at h 11, and 10 at h 18) and a multiple linear model was performed to determine if time post estrous onset impacted metabolite abundance. Results: Metabolites influenced by time post estrous onset were tested for enrichment in KEGG pathways. Ninety metabolites were identified in follicular fluid samples. Twenty metabolites differed in abundance among timepoints post estrous onset (p ≤ 0.05). Pathways corresponding to amino acid and energy metabolism were enriched with metabolites impacted by time post estrous onset (FDR ≤ 0.10). Discussion: Results from the current study indicate early response to the LH surge to increase bioavailability of amino acids and metabolites used by the cumulus and granulosa cells for energy production and shuttled into the oocyte to support meiotic maturation. Such metabolites may later be used by the ovulatory follicle for protein production.

Preovulatory follicle contributions to oocyte competence in cattle: importance of the ever-evolving intrafollicular environment leading up to the luteinizing hormone surge

The preovulatory intrafollicular environment plays a major role in determining oocyte competence. The basis of this review is to highlight the importance of the preovulatory follicle's physiological status prior to the preovulatory luteinizing hormone (LH) surge and onset of oocyte maturation to promote an optimal follicular microenvironment and optimal oocyte developmental competence in cattle. While the underlying mechanisms remain unclear, and are likely multifactorial, the preovulatory follicle's physiological status prior to the preovulatory LH surge is highly influential on the oocyte's capacity to undergo postfertilization embryo development. Changes in the intrafollicular environment of the preovulatory follicle including steroid hormone production, metabolome profiles, and proteome profiles likely support the oocyte's developmental and metabolic competency. This review focuses on the relationship between bovine oocyte developmental competency and antral follicle progression to the preovulatory phase, the role of the preovulatory follicle in improving oocyte developmental competence in cattle, and the importance of the ever-evolving preovulatory intrafollicular environment for optimal fertility.

iTRAQ-Based proteomic dataset for bovine pre-ovulatory plasma and follicular fluid containing high and low Estradiol

This is isobaric tags for a relative and absolute quantification (iTRAQ)-Based Proteomic Data on bovine plasma (PL) and follicular fluid (FF) containing high and low pre-ovulatory circulating concentration of estradiol (E2). The PL and FF were collected from nine beef cows that were identified to initiate a new follicular wave on day -4 during synchronization. Follicular dynamics and ovulatory response were monitored using transrectal ultrasonography. Blood samples were collected at slaughter and FF was aspirated from dominant follicles (DF; >10 mm). Estradiol concentrations in PL and FF were measured by radioimmunoassays. Plasma and FF were labeled as containing high E2 (PL HE2 and FF HE2) or low E2 (PL LE2 and FF LE2). Abundant proteins (albumin, IgG, IgA, and alpha-1-antitrypsin) were depleted from the four PL and FF samples. Peptides were labeled with iTRAQ reagents and analyzed using 2-dimentional liquid chromatography ESI-based mass spectrometry. Proteins were identified and quantified using SEQUEST^TM search engine embedded in Proteome Discoverer. The proteins matched with at least one unique peptide at minimum 95% confidence were considered positive identifications. Protein expression levels were determined by assigned fold change of >2.0 or <0.5 between any pair from the four sample types. The paired comparisons made were PL HE2 and PL LE2, FF HE2 and FF LE2, PL HE2 and FF HE2, and PL LE2 and FF LE2. Protein Analysis Through Evolutionary Relationships (PANTHER) and Database for Annotation, Visualization and Integrated Discovery (DAVID) were used to classify protein functions. This dataset includes the overview of workflow for identification and quantification of proteins and details on 231 proteins identified which includes 103 up- and down-regulate proteins. This dataset can be useful for further probing of the identified regulated proteins to better understand folliculogenesis and ovulation, particularly in bovine. This dataset is related to the article ‘iTRAQ-Based Proteomic Analysis of Bovine Pre-ovulatory Plasma and Follicular Fluid’ by P. A. Afedi, E. L. Larimore, R. A. Cushman, D. Raynie, G. A. Perry. Domestic Animal Endocrinology. https://doi.org/10.1016/j.domaniend.2021.106606